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Enhancing ECM range

yoyo@home - So, 01.08.2020 - 00:00
I'm enhancing the ecm search range for B1=43e6 up to 2000 digits. Some test workunits are already send out with the name ecm_es_*test* and a short deadline of 1 day. Together with this the credit formula was changed.
Kategórie: Novinky z projektov

Behind the Scenes with World Community Grid's Active Projects

World Community Grid - Po, 27.07.2020 - 18:16
Interested in learning more about our monthly calls with the researchers for each active World Community Grid project? You can get updates on our website, in our forum, and via email.
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Scheduled Internet Outage July 28th,2020

Milkyway@Home - So, 25.07.2020 - 20:02
Hey everyone,

On July 28th, our server will be temporarily inaccessible due to a scheduled campus-wide internet outage. As such, job queues may not update for the day. However, everything should return to working order by the next day. We apologize for any inconvenience this may cause.

-Eric
Kategórie: Novinky z projektov

New paper 2/2: GPCRmd uncovers the dynamics of the 3D-GPCRome

GPUGRID - Pi, 24.07.2020 - 18:26
The second paper is Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S. et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods (2020). 10.1038/s41592-020-0884-y here, your computations have been used to build a database of configurations for most types and subtypes of GPCR-class proteins. GPCRs are "do-all" receptors - there are many many subtypes, each with activators and inhibitors. The GPCRmd database provides for the first time a *systematic* coverage of their dynamics. G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations. ... 14310 1 107681600 101936 2 96720000 483287 3 83904600 500240 4 74393800 306281 5 57790200 93201 6 55775200 100499 7 53115400 504924 8 51664600 25378 9 50858600 62100 10 32240000 125700 11 31837000 73475 12 29983200 69336 13 27645800 28899 14 23615800 31053 15 22406800 146761 16 21439600 497873 17 20230600 13127 18 20069400 36684 19 19666400 126468 20 19021600
Kategórie: Novinky z projektov

New paper 1/2: PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulation

GPUGRID - Pi, 24.07.2020 - 18:23
Two recent papers which came out with results from GPUGRID. First, PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, and Gianni De Fabritiis Journal of Chemical Information and Modeling 2020 60 (4), 2314-2324 DOI: 10.1021/acs.jcim.9b01209 In this paper (and the corresponding live system) GPUGRID's computations are used to power a search for elusive (transient) pockets which may become drug targets. Thanks for the contributions! Cryptic pockets are protein cavities that remain hidden in resolved apo structures and generally require the presence of a co-crystallized ligand to become visible. Finding new cryptic pockets is crucial for structure-based drug discovery to identify new ways of modulating protein activity and thus expand the druggable space. We present here a new method and associated web application leveraging mixed-solvent molecular dynamics (MD) simulations using benzene as a hydrophobic probe to detect cryptic pockets. Our all-atom MD-based workflow was systematically tested on 18 different systems and 5 additional kinases and represents the largest validation study of this kind. CrypticScout identifies benzene probe binding hotspots on a protein surface by mapping probe occupancy, residence time, and the benzene occupancy reweighed by the residence time. The method is presented to the scientific community in a web application available via www.playmolecule.org using a distributed computing infrastructure to perform the simulations. List of most-contributing users: User Rank Credits 101936 1 4639746 14310 2 4450949 483287 3 3535477 103037 4 2362054 500240 5 1986559 25378 6 1969784 504924 7 1945416 100499 8 1834758 73475 9 1796967 125700 10 1755579 126468 11 1651313 306281 12 1638950 62100 13 1542475 21233 14 1536750 535400 15 1364758 13127 16 1161000 509733 17 1035000 28899 18 973950 543022 19 971404 89682 20 946350
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Synthetic Compound May Be Useful for Developing Zika Virus Treatment

World Community Grid - Št, 23.07.2020 - 19:43
As the OpenZika research team wrapped up their work on World Community Grid, they identified a promising compound in the ongoing search for Zika treatments.
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Katherine Johnson Memorial Challenge starts July 24th

PrimeGrid - Ut, 21.07.2020 - 05:27
In honor of the life of Katherine Johnson, PrimeGrid will be running a 7-day TRP-LLR challenge from 24 July 20:00 UTC to 31 July 20:00 UTC. Will we end this subproject's 3-year prime drought? Also make sure to read Hidden Figures, a book about Katherine Johnson and some of her contemporaries, for the book club meeting! Doubts? Disputes? Dubieties? Discuss in the forum thread for the challenge: https://www.primegrid.com/forum_thread.php?id=9217
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Thanks for supporting SixTrack at LHC@Home and updates

LHC@home - Ut, 23.01.2018 - 19:08
Dear volunteers,

All members of the SixTrack team would like to thank each of you for supporting our project at LHC@Home. The last weeks saw a significant increase in work load, and your constant help did not pause even during the Christmas holidays, which is something that we really appreciate!

As you know, we are interested in simulating the dynamics of the beam in ultra-relativistic storage rings, like the LHC. As in other fields of physics, the dynamics is complex, and it can be decomposed into a linear and a non-linear part. The former allows the expected performance of the machine to be at reach, whereas the latter might dramatically affect the stability of the circulating beam. While the former can be analysed with the computing power of a laptop, the latter requires BOINC, and hence you! In fact, we perform very large scans of parameter spaces to see how non-linearities affect the motion of beam particles in different regions of the beam phase space and for different values of key machine parameters. Our main observable is the dynamic aperture (DA), i.e. the boundary between stable, i.e. bounded, and unstable, i.e., unbounded, motion of particles.

The studies mainly target the LHC and its upgrade in luminosity, the so-called HL-LHC. Thanks to this new accelerator, by ~2035, the LHC will be able to deliver to experiments x10 more data than what is foreseen in the first 10/15y of operation of LHC in a comparable time. We are in full swing in designing the upgraded machine, and the present operation of the LHC is a unique occasion to benchmark our models and simulation results. The deep knowledge of the DA of the LHC is essential to properly tune the working point of the HL-LHC.

If you have crunched simulations named "workspace1_hl13_collision_scan_*" (Frederik), then you have helped us in mapping the effects of unavoidable magnetic errors expected from the new hardware of the HL-LHC on dynamic aperture, and identify the best working point of the machine and correction strategies. Tasks named like "w2_hllhc10_sqz700_Qinj_chr20_w2*" (Yuri) focus the attention onto the magnets responsible for squeezing the beams before colliding them; due to their prominent role, these magnets, very few in number, have such a big impact on the non-linear dynamics that the knobs controlling the linear part of the machine can offer relevant remedial strategies.

Many recent tasks are aimed at relating the beam lifetime to the dynamic aperture. The beam lifetime is a measured quantity that tells us how long the beams are going to stay in the machine, based on the current rate of losses. A theoretical model relating beam lifetime and dynamic aperture was developed; a large simulation campaign has started, to benchmark the model against plenty of measurements taken with the LHC in the past three years. One set of studies, named "w16_ats2017_b2_qp_0_ats2017_b2_QP_0_IOCT_0" (Pascal), considers as main source of non-linearities the unavoidable multipolar errors of the magnets, whereas tasks named as "LHC_2015*" (Javier) take into account the parasitic encounters nearby the collision points, i.e. the so called "long-range beam-beam effects".

One of our users (Ewen) is carrying out two studies thanks to your help. In 2017 DA was directly measured for the first time in the LHC at top energy, and nonlinear magnets on either side of ATLAS and CMS experiments were used to vary the DA. He wants to see how well the simulated DA compares to these measurements. The second study seeks to look systematically at how the time dependence of DA in simulation depends on the strength of linear transverse coupling, and the way it is generated in the machine. In fact, some previous simulations and measurements at injection energy have indicated that linear coupling between the horizontal and vertical planes can have a large impact on how the dynamic aperture evolves over time.

In all this, your help is fundamental, since you let us carry out the simulations and studies we are interested in, running the tasks we submit to BOINC. Hence, the warmest "thank you" to you all!
Happy crunching to everyone, and stay tuned!

Alessio and Massimo, for the LHC SixTrack team.
Kategórie: Novinky z projektov

LHC@home down-time due to system updates

LHC@home - Ut, 23.01.2018 - 11:19
Tomorrow Wednesday 24/1, the LHC@home servers will be unavailable for a short period while our storage backend is taken down for a system update.

Today, Tuesday 23/1, some of the Condor servers that handle CMS, LHCb and Theory tasks will be down for a while. Regarding the on-going issues with upload of files, please refer to this thread.

Thanks for your understanding and happy crunching!
Kategórie: Novinky z projektov
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